Two‐dimensional (2D) materials such as graphene and hexagonal boron nitride (h‐BN) have attracted interest as a conductor/insulator pair in next‐generation devices because of their unique physical properties; however, the thermal transport at the interfaces must be understood to accurately predict the performance of heterostructures composed of these materials. Time‐domain thermoreflectance (TDTR) is used to estimate the thermal boundary conductance (TBC) at the interface of h‐BN and graphene to be 34.5 (+11.6/−7.4) MW m−2 K−1. The advantage of TDTR is that it does not need to create a large temperature gradient at the interface of heterostructures, but it has not yet been used for h‐BN/graphene interface. Phonon transmission and TBC at the h‐BN/graphene interface are predicted by two different formulations of the diffuse mismatch model (DMM) for anisotropic materials. The analysis of phonon transmission and temperature dependence of TBC establishes the flexural branch in the ab‐plane, and the c‐plane longitudinal acoustic branch of graphene and h‐BN are the dominant contributors when implementing both the DMM models. The methodology developed herein can be used to analyze heterostructures of other 2D materials.